Rename default menu names.
function system_update_8031() {
$map = array(
'navigation' => 'tools',
'management' => 'admin',
'user-menu' => 'account',
'main-menu' => 'main',
);
foreach ($map as $old => $new) {
db_update('menu_links')
->condition('menu_name', $old)
->fields(array(
'menu_name' => $new,
))
->execute();
}
}